At first, Annabeth thought it was just idolization. It made sense. Percy was the first hero he ever met, ever saw, and even at a glace, Annabeth knew he'd idolize him. From what Percy told her and from what she observed in the labyrinth, she figured Percy was seen as the greatest hero ever. After all, the boy was only ten. Kids at ten, demigod or not, needed idols and heroes.
She understood why he'd hate them. He must have thought she was a replacement, that Percy left with his sister and came back with Annabeth. She felt a need to reach out to him, to console him and remind him that there were others in the world, others that cared for him. Or could care if he let them.
When they met again, briefly, during the Battle of Manhattan, she had known, at least part of it. He cared for Percy, enough to follow him and trust him. He had gotten over his grudge, forgave Percy for Bianca's death, and let him in, even if only a little bit. She had no time to think about why.
Annabeth and Percy got together. She had completely forgotten about him at the time, but later, she saw the bitter look of hatred he gave them before disappearing into the underworld. Later, people said he had a crush on her. She had her doubts, but that look of loathing kept her from saying anything. Hated or not, she cared for him, still felt that need to become the sister he had lost at her expense. Challenging that rumor would erase all thoughts of redemption he had for her.
Annabeth was certain the rumor was false when he came back after hearing of the disappearance of Percy. He took one look at her, pity and sadness in his eyes, and promised he'd help look for Percy. But she knew it wasn't a promise to her. It was a promise to himself. He needed to believe Percy could be found.
They saved him from the giants, and all doubt of his love disappeared. Annabeth was certain about it. She caught the looks he gave her, saw how he looked at Percy.
It could no longer be dismissed as a look one gives his hero, his idol. It could only be the look one gave a loved one, someone you love and hate and wish you properly hated.
Annabeth noticed how he probably could have saved her. She noticed how he didn't even glance at her when she fell. But he made promises to Percy. He gave scared, pained looks to Percy. He worried for Percy.
It was not because he knew the horrors of Tartarus but knew she could handle it. It was not because he thought Percy couldn't. It was only because he didn't care if she lived or died there, he cared if Percy did.
When they got out, she noticed the relieved and less reserved looks he gave Percy. She noticed the looks of unease he gave Jason, and the looks Jason returned to him. She knew Jason knew. So she went to talk to him.
First he claimed ignorance. She shot that down quickly. He claimed innocence next. She told him to drop the act. He claimed secrecy, that he would be killed if he told her. She told him she knew. He claimed someone was calling him. She grabbed him and forced the words out. He relented.
She could tell Jason wanted to say it. She could tell he was worried she would judge. She could tell he was worried he'd be killed. She could tell he wanted to do right. She could tell he was tired of keeping secrets. So she let him tell, she let him say it, promised him safety, promised no judging. He told what he knew.
Annabeth knew now, 100% certain, no chance of being wrong. And since she couldn't be wrong, she could act.
The next time they met him, she cornered him. Confronted him. He nearly killed her in anger. He yelled at her. Told her she didn't understand. She tried to. He told her to forget about it. She persisted. He tried everything he could think of, and when she still wanted him to admit it, to tell it to all the world, he did the last thing he ever thought he was going to do.
She lived. Barely, but she lived. And she knew she had made a mistake. He wasn't ready yet. He still wanted to believe that if he tried hard enough, he could hate Percy Jackson, rightly and properly, the way he hated her. So she let him be. She forgot about it. She acted normal, like nothing ever happened. She reached out to him like she always did, and he pushed her away like he always did. Nothing was new. The confrontation never happened.
But she still saw the bitter looks he gave her, the looks so pure of hatred she could never erase from her mind. She still saw the looks of hopeful longing he tried to mask when he looked at Percy. She knew that his efforts to hate remained unfruitful. But she didn't meddle. She let him try and change his emotions, try and hate. She let him hate her, hate Jason, try to hate Percy. She let him hate himself.